To utilize high-capacity Si anodes in next-generation Li-ion batteries, the physical and chemical transformations during the Li-Si reaction must be better understood. Here, in situ transmission electron microscopy is used to observe the lithiation/delithiation of amorphous Si nanospheres; amorphous Si is an important anode material that has been less studied than crystalline Si. Unexpectedly, the experiments reveal that the first lithiation occurs via a two-phase mechanism, which is contrary to previous understanding and has important consequences for mechanical stress evolution during lithiation. On the basis of kinetics measurements, this behavior is suggested to be due to the rate-limiting effect of Si-Si bond breaking. In addition, the results show that amorphous Si has more favorable kinetics and fracture behavior when reacting with Li than does crystalline Si, making it advantageous to use in battery electrodes. Amorphous spheres up to 870 nm in diameter do not fracture upon lithiation; this is much larger than the 150 nm critical fracture diameter previously identified for crystalline Si spheres.